chrX-133596587-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_004484.4(GPC3):āc.1426A>Gā(p.Met476Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000215 in 1,209,296 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M476L) has been classified as Likely benign.
Frequency
Consequence
NM_004484.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPC3 | NM_004484.4 | c.1426A>G | p.Met476Val | missense_variant | 7/8 | ENST00000370818.8 | |
GPC3 | NM_001164617.2 | c.1495A>G | p.Met499Val | missense_variant | 8/9 | ||
GPC3 | NM_001164618.2 | c.1378A>G | p.Met460Val | missense_variant | 7/8 | ||
GPC3 | NM_001164619.2 | c.1264A>G | p.Met422Val | missense_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPC3 | ENST00000370818.8 | c.1426A>G | p.Met476Val | missense_variant | 7/8 | 1 | NM_004484.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000537 AC: 6AN: 111683Hom.: 0 Cov.: 22 AF XY: 0.0000296 AC XY: 1AN XY: 33823
GnomAD3 exomes AF: 0.0000655 AC: 12AN: 183341Hom.: 0 AF XY: 0.0000590 AC XY: 4AN XY: 67823
GnomAD4 exome AF: 0.0000182 AC: 20AN: 1097560Hom.: 0 Cov.: 29 AF XY: 0.0000165 AC XY: 6AN XY: 362928
GnomAD4 genome AF: 0.0000537 AC: 6AN: 111736Hom.: 0 Cov.: 22 AF XY: 0.0000295 AC XY: 1AN XY: 33886
ClinVar
Submissions by phenotype
Wilms tumor 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at